ArticleNucleic acids research2018
EBI Metagenomics in 2017: enriching the analysis of microbial communities, from sequence reads to assemblies.
Article in Nucleic acids research, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 110 papers, 1 of them a synthesis that pooled it.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
110 citing papers in PubMed, 1 synthesis or guideline pooled it.
- MICHELINdb: a web-based tool for mining of helminth-microbiota interaction datasets, and a meta-analysis of current research.Microbiome · 2020Pooled it
- Towards Key Principles of Host-Associated Microbiome Assembly.Ecology letters · 2026Article
- The eco-evolutionary assembly of complex communities with multiple interaction types.Nature communications · 2026Article
- Article
- Metagenomics reveals fibre fermentation and AMR pathways in red grouse (Lagopus scotica) microbiota.BMC microbiology · 2025Article
- Deep Learning Transforms Phage-Host Interaction Discovery from Metagenomic Data.bioRxiv : the preprint server for biology · 2025Article
- Techniques for learning and transferring knowledge for microbiome-based classification and prediction: review and assessment.Briefings in bioinformatics · 2024Review
- Assembling bacterial puzzles: piecing together functions into microbial pathways.NAR genomics and bioinformatics · 2024Article
- Diverse bacterial consortia: key drivers of rhizosoil fertility modulating microbiome functions, plant physiology, nutrition, and soybean grain yield.Environmental microbiome · 2024Article
- A Review of Web-Based Metagenomics Platforms for Analysing Next-Generation Sequence Data.Biochemical genetics · 2024Review
- Enhancing Clinical Utility: Utilization of International Standards and Guidelines for Metagenomic Sequencing in Infectious Disease Diagnosis.International journal of molecular sciences · 2024Review
- Sparse species interactions reproduce abundance correlation patterns in microbial communities.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- NCRD: A non-redundant comprehensive database for detecting antibiotic resistance genes.iScience · 2023Article
- The AnimalAssociatedMetagenomeDB reveals a bias towards livestock and developed countries and blind spots in functional-potential studies of animal-associated microbiomes.Animal microbiome · 2023Article
- Benchmarking Metagenomic Classifiers on Simulated Ancient and Modern Metagenomic Data.Microorganisms · 2023Article
- Environmental fluctuations explain the universal decay of species-abundance correlations with phylogenetic distance.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- A Comprehensive Insight of Current and Future Challenges in Large-Scale Soil Microbiome Analyses.Microbial ecology · 2023Review
- Microbiome-based enrichment pattern mining has enabled a deeper understanding of the biome-species-function relationship.Communications biology · 2023Article
- Bacterial diversity in the aquatic system in India based on metagenome analysis-a critical review.Environmental science and pollution research international · 2023Review
- Capturing variation in metagenomic assembly graphs with MetaCortex.Bioinformatics (Oxford, England) · 2023Article
50 more citing papers are in PubMed but not listed here.
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PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
17 authors.
Funding
Abstract
EBI metagenomics (http://www.ebi.ac.uk/metagenomics) provides a free to use platform for the analysis and archiving of sequence data derived from the microbial populations found in a particular environment. Over the past two years, EBI metagenomics has increased the number of datasets analysed 10-fold. In addition to increased throughput, the underlying analysis pipeline has been overhauled to include both new or updated tools and reference databases. Of particular note is a new workflow for taxonomic assignments that has been extended to include assignments based on both the large and small subunit RNA marker genes and to encompass all cellular micro-organisms. We also describe the addition of metagenomic assembly as a new analysis service. Our pilot studies have produced over 2400 assemblies from datasets in the public domain. From these assemblies, we have produced a searchable, non-redundant protein database of over 50 million sequences. To provide improved access to the data stored within the resource, we have developed a programmatic interface that provides access to the analysis results and associated sample metadata. Finally, we have integrated the results of a series of statistical analyses that provide estimations of diversity and sample comparisons.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.